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- PDB-9fsa: Cell wall anchoring domain of the surface layer protein of Methan... -

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Basic information

Entry
Database: PDB / ID: 9fsa
TitleCell wall anchoring domain of the surface layer protein of Methanococcus voltae (aa 24-75; 484-576)
ComponentsS-layer protein
KeywordsSTRUCTURAL PROTEIN / Surface layer protein / self assembly / cell wall binding / anchoring / symmetry
Function / homologyS-layer protein / S-layer protein, N-terminal / S-layer protein, C-terminal / S-layer like family, central region / S-layer like family, outer domain / S-layer / cell wall organization / extracellular region / S-layer protein
Function and homology information
Biological speciesMethanococcus voltae (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGrininger, C. / Sagmeister, T. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundBioMolStruct doc.fund (DOC130) Austria
CitationJournal: Nat Commun / Year: 2024
Title: SymProFold: Structural prediction of symmetrical biological assemblies.
Authors: Buhlheller, C. / Sagmeister, T. / Grininger, C. / Gubensak, N. / Sleytr, U.B. / Uson, I. / Pavkov-Keller, T.
History
DepositionJun 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer protein


Theoretical massNumber of molelcules
Total (without water)15,7581
Polymers15,7581
Non-polymers00
Water25214
1
A: S-layer protein

A: S-layer protein


Theoretical massNumber of molelcules
Total (without water)31,5162
Polymers31,5162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area1410 Å2
ΔGint-14 kcal/mol
Surface area11650 Å2
Unit cell
Length a, b, c (Å)46.340, 53.268, 55.627
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein S-layer protein / Cell surface glycoprotein / Surface layer protein


Mass: 15757.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus voltae (archaea) / Gene: sla
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q50833
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: JCSG+ eco condition C2 1.0 M LiCl, 0.1 M citrate pH 4.0, 20 % PEG 6000 0.3 ul condition + 0.3 ul protein solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3414 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3414 Å / Relative weight: 1
ReflectionResolution: 2.05→46.34 Å / Num. obs: 4977 / % possible obs: 90.7 % / Redundancy: 23.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.332 / Net I/σ(I): 8.2
Reflection shellResolution: 2.05→2.24 Å / Redundancy: 15.8 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 291 / CC1/2: 0.65 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHENIX1.20.1refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→46.34 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.873 / SU B: 6.53 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.686 / ESU R Free: 0.324
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2825 286 5.75 %
Rwork0.2652 4688 -
all0.266 --
obs-4974 54.725 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.898 Å2
Baniso -1Baniso -2Baniso -3
1--1.316 Å2-0 Å20 Å2
2--0.554 Å2-0 Å2
3---0.762 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 14 942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.012932
X-RAY DIFFRACTIONr_bond_other_d0.0010.016936
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.6091268
X-RAY DIFFRACTIONr_angle_other_deg0.3581.5572164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0475133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.02951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.1610150
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0861028
X-RAY DIFFRACTIONr_chiral_restr0.0440.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02142
X-RAY DIFFRACTIONr_nbd_refined0.2050.2190
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.2974
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2491
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2603
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.219
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.218
X-RAY DIFFRACTIONr_nbd_other0.310.256
X-RAY DIFFRACTIONr_mcbond_it2.1092.172538
X-RAY DIFFRACTIONr_mcbond_other2.1072.172538
X-RAY DIFFRACTIONr_mcangle_it3.5053.229669
X-RAY DIFFRACTIONr_mcangle_other3.5043.235670
X-RAY DIFFRACTIONr_scbond_it2.0542.589394
X-RAY DIFFRACTIONr_scbond_other2.0522.594395
X-RAY DIFFRACTIONr_scangle_it3.5523.717599
X-RAY DIFFRACTIONr_scangle_other3.5493.722600
X-RAY DIFFRACTIONr_lrange_it8.81241.8034017
X-RAY DIFFRACTIONr_lrange_other8.81241.8154017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work% reflection obs (%)WRfactor RworkFsc free
2.05-2.10300.287330.2876450.9265.11630.277
2.103-2.1610.32230.355870.3546390.89314.08450.3150.86
2.161-2.2230.48430.3741290.3766330.90520.85310.360.809
2.223-2.2910.3650.2721470.2755930.94925.63240.2560.918
2.291-2.3660.169150.321730.3085970.93231.49080.3020.96
2.366-2.4490.419130.3022060.3085730.93538.21990.2620.902
2.449-2.5410.322140.3262210.3265430.93243.27810.3120.956
2.541-2.6450.297160.3432360.345330.93247.27950.3090.927
2.645-2.7620.34380.3112620.3125050.93153.46530.2670.85
2.762-2.8960.382190.3292930.3334960.92862.90320.290.909
2.896-3.0520.342220.2983120.3014600.93772.60870.2660.957
3.052-3.2370.348240.2883550.2914540.94183.48020.2390.929
3.237-3.4590.318160.2953800.2964200.94594.28570.2540.925
3.459-3.7340.277230.2493590.2513930.95997.2010.210.951
3.734-4.0880.192140.2363470.2343620.96399.72380.2030.977
4.088-4.5660.157270.1933090.193360.9761000.1760.98
4.566-5.2640.305220.2272740.2322960.9711000.2130.964
5.264-6.4260.358210.2682470.2762680.9521000.2470.939
6.426-9.0020.314150.21900.2052050.9741000.2090.946
9.002-46.340.15360.2341280.231340.9611000.2670.99

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